Biochemistry, Biophysics, and Structural Biology Commons^™

Cloning And Overexpression Of Imp/Osta, An Essential Escherichia Coli Outer Membrane Protein With A Possible Role In Lipid Transport, Leslie Lekatz

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

Activation In Neural Networks Controlling Ingestive Behaviors: What Does It Mean, And How Do We Map And Measure It?, Alan Watts, Arshad Khan, Graciela Sanchez-Watts, Dawna Salter, Christina Neuner

Selected Works Temporary Series

No abstract provided.

Activation In Neural Networks Controlling Ingestive Behaviors: What Does It Mean, And How Do We Map And Measure It?, Watts, Arshad Khan, Graciela Sanchez-Watts, Dawna Salter, Christina Neuner

Departmental Papers (Biology)

No abstract provided.

The Response Of A Biocompatible Liquid Crystal To Ions And Chemistry On Nanostructured Surfaces, Anny Huang

Renée Crown University Honors Thesis Projects - All

Traditional lyotropic liquid crystals are composed of amphiphilic molecules forming assemblies in water. Disodium cromoglycate (cromolyn or DSCG) – an antiasthmatic drug – is a novel and unusual lyotropic liquid crystal because it is not amphiphilic, and yet, it exhibits large birefringence (shininess) when dissolved in water forming lyotropic liquid crystal. In the work, DSCG liquid crystal is doped with different types of salt such as sodium chloride and sodium perchlorate, and the response in the changes of birefringence and liquid crystal transition temperature is studied. We find that addition of certain type of salts enhance the propensity of formation …

Mechanisms Imposing The Vbeta Bias Of V14a Natural Killer T Cells And Consequences For Microbial Glycolipid Recognition, Paul B. Savage, Dasten G. Wei, Shane A. Curran, Luc Teyton, Albert Bendelac

Faculty Publications

Mouse and human natural killer T (NKT) cells recognize a restricted set of glycosphingolipids presented by CD1d molecules, including self iGb3 and microbial alpha-glycuronosylceramides. The importance of the canonical Valpha 14-Jalpha18 TCR alphachain for antigen recognition by NKT cells is well recognized, but the mechanisms underlying the Vbeta8, Vbeta7, and Vbeta2 bias in mouse have not been explored. To study the influences of thymic selection and the constraints of pairing with Valpha 14-Jalpha 18, we have created a population of mature T cells expressing Valpha 14-Jalpha 18 TCRalpha chain in CD1d-deficient mice and studied its recognition properties in vitro and …

Evaluation Of Toxicity Following Electrically Mediated Interleukin-12 Gene Delivery In A B16 Mouse Melanoma Model, Loree Heller, Kathleen Merkler, Jeffrey Westover, Yolmari Cruz, Domenico Coppola, Kaaron Benson, Adil Daud, Richard Heller

Bioelectrics Publications

PURPOSE: Interleukin-12 (IL-12) has potential as an immunotherapeutic agent for the treatment of cancer but is unfortunately associated with toxicity. Delivery of a plasmid encoding IL-12 with electroporation induces an antitumor effect in the B16 mouse melanoma model without serious side effects. To translate this observation to the clinic, an evaluation of toxicity was done in the mouse model.

EXPERIMENTAL DESIGN: Weight change, tumor response, blood chemistry and hematology values, and serum IL-12 levels were evaluated. Multiple tissues were analyzed histopathologically.

RESULTS: A pronounced reduction in tumor volume, including a large percentage of complete regressions, was observed after electrically mediated …

Biogeochemistry Of Arsenic And Antimony In The North Pacific Ocean, Gregory A. Cutter, Lynda S. Cutter

OES Faculty Publications

The biogeochemical cycles of the metalloid elements arsenic and antimony were examined along a 15,000 km surface water transect and at 9 vertical profile stations in the western North Pacific Ocean as part of the 2002 IOC Contaminant Baseline Survey. Results show that the speciation of dissolved arsenic (As III, As V, and methylated As) was subtly controlled by the arsenate (AsV)/phosphate ratio. An additional fraction of presumed organic arsenic previously reported in coastal waters was also present (~15% of the total As) in oceanic surface waters. Dissolved inorganic antimony displayed mildly scavenged behavior that was confirmed by correlations with …

Ethanol Production From Grain, Department Of Agriculture And Food, Western Australia

All other publications

Two methods are currently used to produce ethanol from grain: wet milling and dry milling. The adjectives ‘wet’ and ‘dry’ describe the method, not the product. The different methods affect both the profitability and logistics. Dry mills produce ethanol, distillers' grain and carbon dioxide (Figure 1). The carbon dioxide is a co-product of the fermentation, and the distillers’ dried grain with solubles (DDGS) is a non-animal based, high protein livestock feed supplement, produced from the distillation and dehydration process. If distillers' grains are not dried, they are referred to as distillers' wet grain (DWG). Wet mill facilities are ‘bio-refineries’ producing …

A Sensitive Subject: Haploinsufficiency Of The Yeast Vma13 Gene In Simple And Compound Heterozygotes, Jason Michael Rizzo

Renée Crown University Honors Thesis Projects - All

Vacuolar-proton translocating-ATPases (V-ATPases) are the membranebound transporters responsible for controlling pH levels in intracellular compartments. The V-ATPase enzyme is a multi-subunit complex consisting of two distinct domains, a cytosolic V1 region and a membrane-bound Vo domain. While the interface between V1 and Vo is not as well understood, studies suggest the possibility of multiple peripheral stalks tethering the complex. In response to glucose deprivation, the V1 and Vo sectors of the enzyme are capable of dissociating into separate, and inactive, domains as a means of regulation. At least 4 V1 subunits (C, H, E, and G) are believed to form …

The Role Of Trailerhitch In Mouse Germ Cell Development, Ashley L. O'Hara

Renée Crown University Honors Thesis Projects - All

During oogenesis in the Drosophila ovary, a 16-cell cyst develops in which one cell grows to become the oocyte. The surrounding nurse cells transport mRNAs, proteins, and organelles to the oocyte during development and must be localized properly within the oocyte. A complex of proteins is responsible for mRNA localization, including the recently discovered protein Trailerhitch. Homologs of Trailerhitch exist in other species including C. elegans, yeast, mice, and humans, but the function is unknown. We are interested in studying the function of Trailerhitch in mouse germ cell development. Mice with a nonfunctional Trailerhitch gene were synthesized using a gene …

Total Synthesis Of Pumiliotoxin 341a, Lydia Choi

Renée Crown University Honors Thesis Projects - All

Pumiliotoxin 341 A differs from all other pumiliotoxins in that its alkylidene side chain has been cyclized to form a pyranose ring, providing another quaternary center in its indolizidine ring. Although the gross structure of this natural product has been determined, the absolute and relative stereochemistry of the tertiary alcohol on C14 is still unknown. As a result, we want to synthesize this alkaloid to prove its stereochemistry and to prepare material for further biological analysis. A rhodium-catalyzed alkyne addition reaction currently being developed in our group is employed as the key reaction in our synthesis of the indolizidine core. …

Isolation Of A Ubiquitous Obligate Thermoacidophilic Archaeon From Deep-Sea Hydrothermal Vents, Anna-Louise Reysenbach, Yitai Liu, Amy B. Banta, Terry J. Beveridge, Julie D. Kirshtein, Stefan Schouten, Margaret K. Tivey, Karen L. Von Damm, Mary A. Voytek

Biology Faculty Publications and Presentations

Deep-sea hydrothermal vents are important in global biogeochemical cycles, providing biological oases at the sea floor that are supported by the thermal and chemical flux from the Earth's interior. As hot, acidic and reduced hydrothermal fluids mix with cold, alkaline and oxygenated sea water, minerals precipitate to form porous sulphide–sulphate deposits. These structures provide microhabitats for a diversity of prokaryotes that exploit the geochemical and physical gradients in this dynamic ecosystem. It has been proposed that fluid pH in the actively venting sulphide structures is generally low (pH < 4.5), yet no extreme thermoacidophile has been isolated from vent deposits. Culture-independent surveys based on ribosomal RNA genes from deep-sea hydrothermal deposits have identified a widespread euryarchaeotal lineage, DHVE2 (deep-sea hydrothermal vent euryarchaeotic 2) Despite the ubiquity and apparent deep-sea endemism of DHVE2, cultivation of this group has been unsuccessful and thus its metabolism remains a mystery. Here we report the isolation and cultivation of a member of the DHVE2 group, which is an obligate thermoacidophilic sulphur- or iron-reducing heterotroph capable of growing from pH 3.3 to 5.8 and between 55 and 75 °C. In addition, we demonstrate that this isolate constitutes up to 15% of the archaeal population, providing evidence that thermoacidophiles may be key players in the sulphur and iron cycling at deep-sea vents.

The Fate Of Iron Released From Heme By Hemeoxygenase-1, Jonathan Mark Gardner

Undergraduate Honors Capstone Projects

A strain of Escherichia coli was genetically modified to co-express human heme oxygenase-1 and ferritin. The E. coli were then grown with varying amounts of hemin to see if the iron released upon degradation of the hemin by heme oxygenase-1 is loaded into ferritin. Following incubation, the ferritin was purified and the amount of iron loaded into ferritin determined. It was found that ferritin purifed from E. coli expressing human heme oxygenase-1 contained more iron than E. coli that did not contain human heme oxygenase-1. It was concluded that some of the iron released upon degradation of hemin by heme …

Erratum: "Hard Sphere Radial Distribution Function Again", Andrij Trokhymchuk, Douglas Henderson, Ivo Nezbeda, Jan Jirsak

Faculty Publications

Some misprints have been found for parameters given by Eqs. 29 and 30 and the relevant equations in the Appendix.

Two New Resorcinarenes: A Pyridine & Acetic Acid Ligand For Metal Coordination And A Deep-Cavity Nitroquinoxaline Resorcinarene, Samantha Sizemore Vernetti

Theses and Dissertations

Functionalizing the upper rim of resorcinarene-based cavitands allows a variety of compounds to be synthesized from a single scaffold. Using the upper-rim moieties as ligands for a variety of transition metal ions further increases the versatility of this class of host compounds. A new resorcinarene-based molecule functionalized with four pyridine and acetic acid ligands has been successfully prepared to explore the properties of metal-assembled complexes. To synthesize this compound, tetra(bromomethyl)cavitand was reacted with N-(2-pyridylmethyl)-N-ethylacetate amine to give ethyl acetate pyridine resorcinarene. Hydrolysis of the ester gave acetic acid pyridine resorcinarene (APRes) in good yield. Complexes with Cu2+, Co2+, and Zn2+ …

The Study Of Nitric Oxide Synthase Expression, Function, And Regulation In The Renal Vasculature During Postnatal Renal Development, Brian Blake Ratliff

Theses and Dissertations in Biomedical Sciences

The newborn kidney is vulnerable to vasomotor acute renal failure (ARF) from adverse perinatal events or complications of prematurity. Nitric oxide (NO) vasodilation is vitally protective in this type of ARF, but its relationship with other vasoactive factors, such as angiotensin II (AII) has not been examined. In the immature kidney, nitric oxide synthase (NOS) isoforms, specifically eNOS and nNOS, are developmentally regulated, but their specific role and regulation are unknown.

The enhanced vasodilatory role of NO in the immature kidney was hypothesized to be attributed to regulatory, expressional, and functional differences in eNOS and nNOS isoforms from the adult. …

Biochemical Profiling Of Gout Patients, Tamera Fayre Schlitt

Chemistry & Biochemistry Theses & Dissertations

The purpose of the research is to investigate the biochemical cause of gout in 82 patients. The gouty patients had been diagnosed with gout according to the criterion of the American Rheumatism Association. This gout patient population consisted of 58 men and 24 women with gout whose ages ranged from 11 to 84 years of age with a mean age of 44 years. Key purine metabolism enzyme activity levels and purine metabolite concentrations in the patients' plasma and urine were compared to the mean values of a healthy control group. The control group consisted of 33 males and 25 female …

Aspartyl-Trna Synthetase Is The Target Of Peptidenucleotide Antibiotic Microcin C, Anastasia Metlitskaya, Teymur Kazakov, Aigar Kommer, Olga Pavlova, Mette Praetorius-Ibba, Michael Ibba, Igor Krasheninnkov, Vyacheslav Kolb, Inessa Khmel, Konstantin Severinov

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Microcin C is a ribosome-synthesized heptapeptide that contains a modified adenosine monophosphate covalently attached to the C-terminal aspartate. Microcin C is a potent inhibitor of bacterial cell growth. Based on the in vivo kinetics of inhibition of macromolecular synthesis, Microcin C targets translation, through a mechanism that remained undefined. Here, we show that Microcin C is a subject of specific degradation inside the sensitive cell. The product of degradation, a modified aspartyl-adenylate containing an N-acylphosphoramidate linkage, strongly inhibits translation by blocking the function of aspartyl-tRNA synthetase.

Gas Chromatography: Mass Spectrometry Of Chemical Agents And Related Interferents, Lailiang Zhai

Theses and Dissertations

One of the main problems encountered in chemical analysis operations in the field is collecting sufficient sample from the source and transferring that sample to the measurement instrument for fast separation and identification. I have been involved in developing a field-portable gas chromatography-mass spectrometry (GC-MS) system with solid phase microextraction (SPME) sampling for point detection of chemical agents. The objective is to minimize the analysis time between sampling and detection of a potential chemical threat. SPME offers a convenient means for sampling gaseous and liquid samples, concentrating the analytes, and transferring the analytes to the injection port of a GC …

Development Of An Unbiased Statistical Method For The Analysis Of Unigenic Evolution, Colleen D. Behrsin, Chris J. Brandl, David W. Litchfield, Brian H. Shilton, Lindi M. Wahl

Biochemistry Publications

Background: Unigenic evolution is a powerful genetic strategy involving random mutagenesis of a single gene product to delineate functionally important domains of a protein. This method involves selection of variants of the protein which retain function, followed by statistical analysis comparing expected and observed mutation frequencies of each residue. Resultant mutability indices for each residue are averaged across a specified window of codons to identify hypomutable regions of the protein. As originally described, the effect of changes to the length of this averaging window was not fully eludicated. In addition, it was unclear when sufficient functional variants had been examined …

Membrane-Based Protein Preconcentration Microfluidic Devices, Yi Li

Theses and Dissertations

Interest in microchip capillary electrophoresis (CE) is growing due to the rapid analysis times provided and small sample input requirements. However, higher-concentration samples are typically needed because of the small (~pL) detection volumes in these devices. I have made membrane-based protein preconcentration systems in capillary and microchip designs to increase the detectability of low-concentration biological samples. A photopolymerized ion-permeable membrane interfaced with a microchannel in poly(methyl methacrylate) (PMMA) formed the preconcentrator. When a voltage was applied between the sample reservoir and the ionically conductive membrane in a capillary-based system, R-phycoerythrin was concentrated more than 1,000 fold, as determined by laser-induced …

Three-Dimensional Structure Of The Bacterial Cell Wall Peptidoglycan, Samy O. Meroueh, Krisztina Z. Bencze, Dusan Hesek, Mijoon Lee, Timothy L. Stemmler, Shahriar Mobashery

Biochemistry and Molecular Biology Faculty Publications

The 3D structure of the bacterial peptidoglycan, the major constit- uent of the cell wall, is one of the most important, yet still unsolved, structural problems in biochemistry. The peptidoglycan comprises alternating N-acetylglucosamine (NAG) and N-acetylmu- ramic disaccharide (NAM) saccharides, the latter of which has a peptide stem. Adjacent peptide stems are cross-linked by the transpeptidase enzymes of cell wall biosynthesis to provide the cell wall polymer with the structural integrity required by the bacte- rium. The cell wall and its biosynthetic enzymes are targets of antibiotics. The 3D structure of the cell wall has been elusive because of its …

Hydrographic Observations During The 2002 Ioc Contaminant Baseline Survey In The Western Pacific Ocean, C. I. Measures, Greg A. Cutter, W. M. Landing, R. T. Powell

OES Faculty Publications

The 2002 IOC Contaminant Baseline Survey in the western Pacific Ocean was the fourth in a series of cruises intended to establish the contemporary concentrations of trace elements and other materials in the major water masses of the ocean and to illuminate the pathways by which materials delivered to the surface ocean are incorporated in the subsurface waters. The expedition occupied 9 vertical profile stations encompassing the subtropical and subarctic gyre of the western North Pacific. In addition, underway surface water samples were collected during transits between the stations. This paper uses the temperature, salinity, nutrient, oxygen, and chlorophyll data …

Measurement, Characterization, And Source Apportionment Of The Major Chemical Components Of Fine Particulate Material, Including Semi-Volatile Species, Brett D. Grover

Theses and Dissertations

The promulgation of revised standards for atmospheric fine particles (PM2.5) by the US EPA has sparked renewed interest in the ability to accurately measure and characterize suspended atmospheric particulate matter. Semi-volatile material (SVM), consisting of ammonium nitrate and semi-volatile organic material (SVOM), is not accurately measured by EPA accepted methods such as the Federal reference method (FRM) or Tapered Element Oscillating Microbalance (TEOM). However, SVM is often a major fraction of urban aerosols. Recent advances in atmospheric sampling instrumentation allowed for the semi-continuous characterization of urban PM2.5, including SVM. The Filter Dynamic Measurement System (FDMS) was shown to measure total …

Characterization, Functionalization And Applications Of Alkyl Monolayers On Silicon Surfaces, Guilin Jiang

Theses and Dissertations

Investigations were performed on the stability, mechanism of formation and an application of alkyl monolayers chemomechanically prepared on silicon surfaces. A new method of surface modification, laser-activation modification of surfaces (LAMS), and multivariate analyses of time-of-flight secondary ion mass spectrometry (ToF-SIMS) images of LAMS spots were also reported. X-ray photoelectron spectroscopy (XPS) and other data show that alkyl monolayers prepared by scribing silicon under 1-iodoalkanes and 1-alkenes were stable over extended periods of time to air, water, a boiling acid and Al Ka X-rays. The stability is attributed to direct Si-C bonding in the monolayers. The observation that the oxygen …

C To U Editing Stimulates A To I Editing In The Anticodon Loop Of A Cytoplasmic Threonyl Trna In Trypanosoma Brucei, Mary Anne T. Rubio, Frank L. Ragone, Kirk W. Gaston, Michael Ibba, Juan D. Alfonzo

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Editing of tRNAs is widespread in nature and either changes the decoding properties or restores the folding of a tRNA. Unlike the phylogenetically disperse adenosine (A) to inosine (I) editing, cytosine (C) to uridine (U) editing has only been previously described in organellar tRNAs. We have shown that cytoplasmic tRNA^Thr(AGU) undergoes two distinct editing events in the anticodon loop: C to U and A to I. In vivo, every inosine-containing tRNA^Thr is also C to U edited at position 32. In vitro, C to U editing stimulates conversion of A to I at the wobble base. Although …

Watershed Assessment Of Long Pond North [Presentation], Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: Long Pond, North (2006, 1994)

No abstract provided.

A Watershed Analysis Of Long Pong North: Implications For Water Quality And Land-Use Management, Colby Environmental Assessment Team, Colby College, Problems In Environmental Science Course (Biology 493), Colby College

Colby College Watershed Study: Long Pond, North (2006, 1994)

The Colby Environmental Assessment Team (CEAT) investigated the water quality of Long Pond North, located in the Belgrade Lakes region of Maine, from June through December 006. CEAT analyzed several physical, chemical, and biological water quality parameters to determine the current health of the lake. Attributes of the watershed such as land-use patterns and residential and commercial development were also studied to determine their impact on water quality. Data collected were used to produce models of the watershed that enabled CEAT to identify possible sources of degradation to the current and future water quality of Long Pond. To examine historic …

Effect Of Geometry Of Molecules On Penetrability Of Fungal Wall And Antifungal Activity Of Cooper(Ii) Biscomplexes Of Substituted 8-Quinolinols And Their 2-Methyl Analogues / Herman Gershon, Muriel Gershon, And Donald D. Clark Harding Laboratory, The New York Botanical Garde, Fordham University, Bronx, New York 10458, Usa, Herman Gershon, Muriel Gershon, Donald Dudley Clarke Phd

Chemistry Faculty Publications

It was shown that the lack of fungitoxicity of some classes of square planar compounds can be altered by adding substituents that make the potential toxicant non-planar and/or dipolar. Corrections were made of errors in a number of published papers. Calculations were made to approximate the sizes and shapes of the perforations in the fungal wall

Epichlorohydrin Cross-Linking Of Synthetic Dna Oligomers, Rami W. Zaharan, Julie T. Millard

Undergraduate Research Symposium (UGRS)

Epichlorohydrin (ECH), an important chemical in the synthetic polymer industry, is a bifunctional alkylating agent with the potential to form DNA interstrand crosslinks. Occupational exposure to this suspect carcinogen leads to chromosomal aberrations, and ECH has been shown to undergo reaction with DNA in vivo and in vitro. We are using denaturing polyacrylamide gel electrophoresis to assess cross-linking of synthetic DNA oligomers by both ECH and the related compound, epibromohydrin (EBH). Both epihalohydrins produce a low-mobility band on denaturing gels consistent with an interstrand cross-link. Moreover, the efficiencies, sequence preferences, reaction kinetics, and pH dependence differ for the two compounds, …